User:Karl E. Zahn/Sandbox RB69 1/fingers-domain



The fingers domain of RB69 DNA pol exist as an insertion between the two sequences forming the palm. Since the fingers domain experiences a 60 degree rotation from the open or apo structure to the closed catalytically competent structure, the fact that the palm flanks the fingers in primary sequence is likely required for proper communication between these domains. The fingers domain also provides important basic residues (K560, K486, R482) that bind triphosphates. K560 is also believed to stabilize the pentacovalent intermediate formed with nucleophilic attack of the 3'-OH on the alpha phosphate.

An additional role, potentially under investigated at this time is the role of the fingers domain in stabilizing the template DNA strand. The residue W574 provides stacking interactions upstream of the templating position.